As the story begins, the Justice League attend the funeral of Sue Dibny, the wife of the superhero, the Elongated Man. The League investigates the scene of the murder, the Dibny household, and are bewildered in the lack of evidence to be found. While sending out most of the League and the Teen Titans to look for fire and/or teleport based villains, the core members of the League secretly turn their attention to small-time villain, Dr. Light (the male one, not to be confused with the woman superhero who debuted in the Crisis). But before they can confront them, Wally West and Kyle Rayner overhear the League's plans and demand to know why they are confronting Light.

The story goes that Dr. Light managed to teleport to the League's satellite and discovered Sue alone and proceededto rape her. Light is stopped quickly, but uncontrollable, swearing he will do it again. The League then decides to wipe his memory and change his personality so the threat is defused. As we later see, the Green Arrow, who is explaining, left out the part where Batman's mind was wiped of the moment when he tried to stop the mindwipe.

Dr. Light discovers he's a target and hires Deathstroke, but in the tail end of the fight, Light regains his memories and escapes, revealing the truth in an optic construct only the Flash is fast enough to see. Sue's autopsied and it is revealed she didn't actually burn to death. Jean Loring (ex-wife of Ray Palmer, aka The Atom) is nearly lynched by an unknown assailant and Lois Lane is threatened by someone who knows she married Superman. Tim Drake goes through a parental struggle with his father, who knows Tim is Robin and wishes for his safety. Captain Boomerang reconnects with his bastard son and discovered he is a speedster. While the divorced Atom and Jean reconnect, Jack Drake, Tim's father is sent a gun with a warning and attacked. Jack uses the gun to kill his attacker, Captain Boomerang, but is killed by one of Boomerang's weapons.

Robin and Boomerang Jr. both lose their fathers and the mystery is apparently solved... Until the autopsy of Sue reveals tiny footprints in her brain, which really killed her. Batman learns of this and deduces also that the Atom didn't kill Sue, and we learn that Jean discovered one of Atom's spare suits. In an attempt to reconnect with Ray, her ex-husband, Jean tried to organize an illusion of a threat to superhero families, but accidentally killed Sue and hired the wrong assassin for Jack Drake. Ray commits Jean to Arkham Asylum and shrinks to a microscopic size and disappears completely.

In the end, the League is shaken up, it is implied that Batman might know he was mind-wiped, Dr. Light regains his old personality, Boomerang's son becomes the new Captain Boomerang, and Ralph Dibny is now a widower.

So in the end, where the Crisis and Zero Hour were large crossovers that involved retconning and large gigantic battles, Identity Crisis was much more low key, being a quieter crossover that was instead a murder mystery. However, that is why fans would point to this book if a new reader ever asked for a good starting point to get into The DCU. The retcons were smaller, but a little obvious. Especially with the Justice League.

It is important to know that the point of this story (at least now) isn't that it's supposed to be an "awesome story", but rather it is something that one isn't supposed to like, since it is a means to remove the rose colored glasses from the readers about the past and the present DCU.

However, fan response to this comic was still highly split. It is worth pointing out Joss Whedon liked it enough to write the foreword for the trade paper back.

Identity Crisis was directly followed by Infinite Crisis, which followed the typical format much more closely.

Tropes used in or associated with Identity Crisis:

Adaptational Badass: Deathstroke the Terminator goes from a Crazy-Prepared, highly-trained and slightly augmented Badass to a superhuman with reflexes that can allow him to "surprise" The Flash with a sword thrust behind Slade's back. That would be the Wally West Flash who once had time slow to a standstill when a sniper's bullet touched his neck.

Adult Fear: The superhero equivalent to a government witness' alias being blown, and your enemies knowing who you are and how to hurt you at your most vulnerable: your loved ones.

Artistic License – Nuclear Physics: A nuclear-powered character (Firestorm) is skewered by a sword. He has to fly off to prevent himself from killing his allies, as "They all know what happens when you puncture a nuclear reactor", and he is shown exploding. Except, as Greg Morrow notes, not much actually happens if you puncture a nuclear reactor. (Further flavoring the inaccuracy stew is that the character's powers were never shown to work that way previously; he had nuclear abilities, but was not a "nuclear reactor".)

Bait and Switch: The penultimate issue had Dr. Mid-Nite discovering a pair of tiny footprints in Sue's brain, suggesting it was the Atom who killed Sue. The issue closes with Ray Palmer and Jean Loring together, Ray wearing a very sinister-looking smile on his face. The next issue reveals that it was Jean, not Ray, who was the culprit.

Berserk Button: Deathstroke goes totally nonlinear when Ollie sticks an arrow in his (blind) eye. Calm and collected the first moment, completely insane the next.

Darker and Edgier: With the DCU already being darker and edgier in most places, one might say that Identity Crisis is far more realistic. The heroes and villains are weaker than usual and the fight scenes don't last for too long.

Death by Secret Identity: We learn that during The Silver Age of Comic Books and The Golden Age of Comic Books, villains learned superheroes' secret identities all the time. Heroes toed the line of the Moral Event Horizon by using Zatanna to make them forget, and neglecting to tell the more principled heroes; such as Superman, Batman, and Wonder Woman; who are also implied to have an inkling that something fishy is going on, but refuse to investigate why villains mysteriously keep forgetting their identities.

Downer Ending: Even catching the villain doesn't make the ending any brighter.

Dropped a Bridge on Him: Firestorm's death really comes out of nowhere, has no bearing on the plot, and seems only to exist so that a superhero dies in the book to give it more dramatic weight. Then it never gets mentioned again in the book after the one page scene. The event was later followed up on in Manhunter, where the League tracks down his killer, but most people didn't know about that tie-in.

It wasn’t a glorious or heroic death. Ronnie was killed by the Shadow Thief using The Shining Knight’s sword. It was a minor scuffle, the kind superheroes partake in all the time. Brad Meltzer’s intention with this scene was to show that sometimes heroes die a quiet, accidental death on the job.

Freak Out: You can pinpoint the moment when Jean snaps completely in the flashback after she accidentally kills Sue (originally wanting only to attack but not seriously injure her), in a single facial expression hyperventilating and sobbing while grinning maniacally, preparing to burn Sue in order to cover it up. Her resulting complete insanity results in two more deaths.

Genre Savvy: While some villains are happy to the news of Sue's murder, other villains are smart enough to realize that this would only led to a witch hunt from the superhero community against the supervillains. Captain Cold even makes a point to have him and The Rogues send their condolences to try to set themselves apart from the crime.

Idiot Ball: A superhuman search for evidence lead by "The World's Greatest Detective" doesn't check the phone records. Of course, no one would have seriously suspected Jean at the time, and she could easily have explained it, considering they knew each other, but no mention of her call is made.

I Never Said It Was Poison: In the last issue, Ray Palmer relaxes with Jean Loring. Jean offhandedly asks about where a certain note (which warned of Captain Boomerang's impending attempt on Jack Drake's life) came from. Ray, horrified, knows Batman had confiscated the note before it could get in the news. When he grills Jean about this, she confesses to killing Sue and hiring Boomerang and Calculator.

It Gets Easier: Jean clearly has a Freak Out after she accidentally kills Sue Dibny, but after that she has little problem setting up Jack Drake to kill Captain Boomerang, and when that results in Drake's death as well she doesn't seem all too bothered in The Reveal.

My Eyes Are Up Here: Subverted and Lampshaded with Slipknot. Green Arrow notes he's smart enough that his eyes are not on Wonder Woman's "famous rack", but on her hip - where her Magic Lasso is.

Mythology Gag: If you look closely at Sue's funeral, you can see Jack Knight standing next to Stargirl. This is actually Jack's last known appearance after retiring at the end of his series; as the Dibnys were key characters in Starman, it's fitting to have him here. He's pointedly not in his old uniform.

Stuffed In The Fridge: Sue. Mind you, it is a murder mystery, presumably someone had to get killed off to motivate the story, someone close to a superhero. However, that someone just had to be a superhero's wife. Also Jack Drake.

Sudden Sequel Heel Syndrome: Jean Loring goes completely off her rocker to try and win back the affection of her ex-husband, Ray Palmer.

Tomato Surprise: Batman's role in the Dr. Light incident and the subsequent mind-wipe when he objected.

Weirdness Censor: When Wally West and Kyle Rayner ask how the inner circle managed to keep their memory-wiping exploits a secret from everyone else (especially Clark Kent and Bruce Wayne, who would probably kick them out of the league if they knew) Green Arrow says that the others "only hear what they want to hear." The conversation takes place not ten feet away from Superman - one panel is on his ear, but he's obviously not paying attention.

What the Hell, Hero?: A few, but the biggest being The Flash when he learns they wiped Batman's memory. And then the Flash lied to Superman about why the group was chasing Dr. Light. And then after finding out the whole story, he still doesn't tell anyone out of respect for Barry; who was implied to have been motivated by Iris' death) and Hal.

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